chr3-43690745-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001346468.2(ANO10):c.-12+772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 426,546 control chromosomes in the GnomAD database, including 174 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001346468.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO10 | NM_001346468.2 | c.-12+772G>A | intron_variant | Intron 1 of 12 | NP_001333397.1 | |||
ANO10 | NM_001346469.2 | c.-12+772G>A | intron_variant | Intron 1 of 11 | NP_001333398.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANO10 | ENST00000428831.1 | c.-236G>A | 5_prime_UTR_variant | Exon 1 of 4 | 5 | ENSP00000406712.1 | ||||
ANO10 | ENST00000436073.1 | c.-307G>A | 5_prime_UTR_variant | Exon 1 of 3 | 4 | ENSP00000404988.1 | ||||
ANO10 | ENST00000413397.5 | c.-12+772G>A | intron_variant | Intron 1 of 3 | 4 | ENSP00000399103.1 |
Frequencies
GnomAD3 genomes AF: 0.0211 AC: 3207AN: 152198Hom.: 55 Cov.: 33
GnomAD4 exome AF: 0.0253 AC: 6932AN: 274230Hom.: 119 Cov.: 2 AF XY: 0.0266 AC XY: 3770AN XY: 141602
GnomAD4 genome AF: 0.0211 AC: 3212AN: 152316Hom.: 55 Cov.: 33 AF XY: 0.0214 AC XY: 1594AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at